On
21 September, 1999, Sander went to Dili, East Timor, on a
reporting mission. That same day, he was brutally murdered.

After a thorough investigation under UN flag, it has become clear that Sander has been murdered in cold blood by two officers of the Indonesian army, major Jakob Djoko Sarosa and lieutenant Camillo Dos Santos on Becora Road in Dili. Sander was executed lying on the ground, after he had fallen off the back of a taxi motorbike he was riding to visit the Becora district, where he was going to gather some quotes of people in the street. The case of the murder of Sander Thoenes is one of the many cases that has been under investigation by the UN Serious Crimes unit in East Timor. In the words of a closely involved policeman: this is a clear-cut case. Even so, a trial has up to now been effectively blocked by Indonesian pressure on the East Timor government. The murderers were never brought to justice.